From owner-freebsd-pkg-fallout@freebsd.org Tue Jan 14 12:57:46 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 008A51E9A50 for ; Tue, 14 Jan 2020 12:57:46 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 47xr8n70rdz46Wt for ; Tue, 14 Jan 2020 12:57:45 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id F062E1E9A4F; Tue, 14 Jan 2020 12:57:45 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id F02241E9A4E for ; Tue, 14 Jan 2020 12:57:45 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 47xr8n6pHMz46Ws; Tue, 14 Jan 2020 12:57:45 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id E4B9F1DE93; Tue, 14 Jan 2020 12:57:45 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (localhost [127.0.0.1]) by beefy18.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 00ECvjMX064129; Tue, 14 Jan 2020 12:57:45 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 00ECvjUf064128; Tue, 14 Jan 2020 12:57:45 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 14 Jan 2020 12:57:45 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202001141257.00ECvjUf064128@beefy18.nyi.freebsd.org> To: mzaki@e-mail.ne.jp Subject: [package - head-amd64-default][biology/muscle] Failed for muscle-3.8.1551 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 14 Jan 2020 12:57:46 -0000 You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: mzaki@e-mail.ne.jp Last committer: fernape@FreeBSD.org Ident: $FreeBSD: head/biology/muscle/Makefile 522911 2020-01-13 17:42:22Z fernape $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p522982_s356710/logs/muscle-3.8.1551.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p522982_s356710 Log: =>> Building biology/muscle build started at Tue Jan 14 12:57:21 UTC 2020 port directory: /usr/ports/biology/muscle package name: muscle-3.8.1551 building for: FreeBSD head-amd64-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300076 amd64 maintained by: mzaki@e-mail.ne.jp Makefile ident: $FreeBSD: head/biology/muscle/Makefile 522911 2020-01-13 17:42:22Z fernape $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300062 Jail OSVERSION: 1300076 Job Id: 06 !!! Jail is newer than host. (Jail: 1300076, Host: 1300062) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300076 UNAME_v=FreeBSD 13.0-CURRENT 1300076 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/muscle" EXAMPLESDIR="share/examples/muscle" DATADIR="share/muscle" WWWDIR="www/muscle" ETCDIR="etc/muscle" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/muscle DOCSDIR=/usr/local/share/doc/muscle EXAMPLESDIR=/usr/local/share/examples/muscle WWWDIR=/usr/local/www/muscle ETCDIR=/usr/local/etc/muscle --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300076 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License PD accepted by the user =========================================================================== =================================================== ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [head-amd64-default-job-06] Installing pkg-1.12.0... [head-amd64-default-job-06] Extracting pkg-1.12.0: .......... done ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of muscle-3.8.1551 =========================================================================== =================================================== =========================================================================== =================================================== ===> License PD accepted by the user => muscle_src_3.8.1551.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz muscle_src_3.8.1551.tar.gz 185 kB 973 kBps 00s ===> Fetching all distfiles required by muscle-3.8.1551 for building =========================================================================== =================================================== ===> License PD accepted by the user ===> Fetching all distfiles required by muscle-3.8.1551 for building => SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License PD accepted by the user ===> Fetching all distfiles required by muscle-3.8.1551 for building ===> Extracting for muscle-3.8.1551 => SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for muscle-3.8.1551 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for muscle-3.8.1551 =========================================================================== =================================================== ===> muscle-3.8.1551 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-amd64-default-job-06] Installing gmake-4.2.1_3... [head-amd64-default-job-06] `-- Installing gettext-runtime-0.20.1... [head-amd64-default-job-06] | `-- Installing indexinfo-0.3.1... [head-amd64-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o 3 warnings generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] switch (g_PPScore) ^ c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] switch (OS) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] return (Seq &) *((Seq *) 0); ^~~~~~~~~~~~ c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o subfams.cpp:4:13: error: functions that differ only in their return type cannot be overloaded const float INFINITY = float(1e29); ~~~~~ ^ /usr/include/math.h:58:18: note: expanded from macro 'INFINITY' #define INFINITY __builtin_inff() ^ subfams.cpp:4:13: note: previous implicit declaration is here /usr/include/math.h:58:18: note: expanded from macro 'INFINITY' #define INFINITY __builtin_inff() ^ 1 error generated. gmake[1]: *** [Makefile:32: subfams.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/muscle/work/muscle-3.8.1551' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/muscle